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Title: Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events

Abstract

Sugarcane ( Saccharum spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80–90% of the genome from S. officinarum and 10–20% of the genome from S. spontaneum. We constructed bacterial artificial chromosome (BAC) libraries of S. officinarum variety LA Purple (2n = 8x = 80) and S. spontaneum haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two Saccharum BAC libraries. A total of 5,847,280 bp sequence from S. officinarum and 5,011,570 bp from S. spontaneum were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in S. spontaneum BACs than in S. officinarum BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between Saccharum and Sorghum bicolor and between S. officinarum and S. spontaneum. In the syntenic regions, S. spontaneummore » showed expansion relative to S. officinarum, and both S. officinarum and S. spontaneum showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the Saccharum BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between S. officinarum and S. spontaneum. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 S. officinarum and 1 S. spontaneum BACs revealed that the S. spontaneum intergenic region was distant to those from the 3 homologous regions in S. officinarum. Our results suggested that S. officinarum and S. spontaneum experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.« less

Authors:
 [1];  [2];  [1];  [1];  [3];  [2];  [2];  [4];  [5]
+ Show Author Affiliations
  1. Texas A & M Univ., Dallas, TX (United States). Texas A&M AgriLife Research and Extension Center
  2. Fujian Agriculture and Forestry Univ., Fuzhou (China)
  3. Texas A & M Univ., Weslaco, TX (United States). Texas A&M AgriLife Research Center
  4. Fujian Agriculture and Forestry Univ., Fuzhou (China); Univ. of Illinois at Urbana-Champaign, Champaign, IL (United States)
  5. Texas A & M Univ., Dallas, TX (United States). Texas A&M AgriLife Research and Extension Center; Fujian Agriculture and Forestry Univ., Fuzhou (China); Texas A & M Univ., College Station, TX (United States)
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, Champaign, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1473722
Alternate Identifier(s):
OSTI ID: 1510518
Grant/Contract Number:  
SC0010686
Resource Type:
Published Article
Journal Name:
Frontiers in Plant Science
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1664-462X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; sugarcane; Saccharum; polyploidization; genetic divergence; retrotransposon

Citation Formats

Sharma, Anupma, Song, Jinjin, Lin, Qingfan, Singh, Ratnesh, Ramos, Ninfa, Wang, Kai, Zhang, Jisen, Ming, Ray, and Yu, Qingyi. Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events. United States: N. p., 2018. Web. doi:10.3389/fpls.2018.01414.
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Sharma, Anupma, Song, Jinjin, Lin, Qingfan, Singh, Ratnesh, Ramos, Ninfa, Wang, Kai, Zhang, Jisen, Ming, Ray, & Yu, Qingyi. Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events. United States. doi:10.3389/fpls.2018.01414.
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Sharma, Anupma, Song, Jinjin, Lin, Qingfan, Singh, Ratnesh, Ramos, Ninfa, Wang, Kai, Zhang, Jisen, Ming, Ray, and Yu, Qingyi. Tue . "Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events". United States. doi:10.3389/fpls.2018.01414.
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@article{osti_1473722,
title = {Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events},
author = {Sharma, Anupma and Song, Jinjin and Lin, Qingfan and Singh, Ratnesh and Ramos, Ninfa and Wang, Kai and Zhang, Jisen and Ming, Ray and Yu, Qingyi},
abstractNote = {Sugarcane (Saccharum spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80–90% of the genome from S. officinarum and 10–20% of the genome from S. spontaneum. We constructed bacterial artificial chromosome (BAC) libraries of S. officinarum variety LA Purple (2n = 8x = 80) andS. spontaneum haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two Saccharum BAC libraries. A total of 5,847,280 bp sequence from S. officinarum and 5,011,570 bp fromS. spontaneum were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in S. spontaneum BACs than in S. officinarum BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between Saccharum and Sorghum bicolor and between S. officinarum and S. spontaneum. In the syntenic regions, S. spontaneum showed expansion relative to S. officinarum, and both S. officinarum and S. spontaneum showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the Saccharum BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between S. officinarum and S. spontaneum. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 S. officinarum and 1 S. spontaneum BACs revealed that the S. spontaneum intergenic region was distant to those from the 3 homologous regions in S. officinarum. Our results suggested that S. officinarum and S. spontaneum experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.},
doi = {10.3389/fpls.2018.01414},
journal = {Frontiers in Plant Science},
number = ,
volume = 9,
place = {United States},
year = {2018},
month = {9}
}
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DOI: 10.3389/fpls.2018.01414
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